RetrogeneDB ID: retro_mmul_1806

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:152880402..152881051(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000016705
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.2291
• Ensembl ID: ENSMMUG00000019630
• Aliases: None
• Description: glutathione S-transferase mu 2 (muscle) [Source:RefSeq peptide;Acc:NP_001248580]

Sequence

>retro_mmul_1806
CCCATGACACAGGGGTACTGGGACATCTGAGGGCTGACCCACACCATCTGCCTGCTCCAGCAATACACAGACTCAAGCTA
TGAGGAAAAGAAGCACACGATGGGGGGGTGCTCCTGACTCTGACAGAAGCCAGTGGTTGAATGAAAAAGTTGAGCTAGGC
CTGGACTTTCCCAATCTGCCCTACTTGACTGATGGGGCTCACAAGATAACCCAGAGCAAGGCCATCCTGGGCTGCATTGC
CTACAAGCACAACCTGTGTGGGGAGACAGAAAGGGAGAAGATTTGGGAAGACAGTTTGGAGAACCAGCTTATGGACAACC
AAATGCAGCTGGCCAGACTCTGCTACAACGCAGGTTCTGAGAAACTGAAGCCAGAATATCTGGAGGCACTCCCTGCAATG
CTGAAATTCTACTCACAGTTTCTGGGGAAGCAGCCATGGTTTCTTGGGGACAAGATCGCCCTTGTGGATTTCATTGCTTA
TGATGTCCTTGAGAGAAACCAAGTATTTGAGCCCAAGTGCTTGGATGCTTTCCCAAACCTGAAGGACTTCATCTCCCGAT
TTGAGGGCTTGGAGATCTCTGCCTACACGAAATCCAGCCGCTTCCTCCCAAGACCTGTGTTCACAAAGATGGCTGTCTGG
GGCAACAAG

Alignment

ORF - retro_mmul_1806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.03 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PMTLGYWNIRGLAHSIRLLLEYTGSSYEEKKYTMGD-APDYDRSQWLNEKFKLGLDFPNLPYLIDGTHKI
          PMT.GYW.I.GL.H.I.LL..YT.SSYEEKK.TMG..APD.DRSQWLNEK..LGLDFPNLPYL.DG.HKI
Retrocopy PMTQGYWDI*GLTHTICLLQQYTDSSYEEKKHTMGG>APDSDRSQWLNEKVELGLDFPNLPYLTDGAHKI

Parental  TQSNAILRYIARKHNLCGETEKEKIREDILENQLMDNRMQLARLCYDPDFEKLKPEYLEGLPEMLKLYSQ
          TQS.AIL..IA.KHNLCGETE.EKI.ED.LENQLMDN.MQLARLCY....EKLKPEYLE.LP.MLK.YSQ
Retrocopy TQSKAILGCIAYKHNLCGETEREKIWEDSLENQLMDNQMQLARLCYNAGSEKLKPEYLEALPAMLKFYSQ

Parental  FLGKQPWFLGDKITFVDFIAYDVLERNQVFEPSCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFT
          FLGKQPWFLGDKI..VDFIAYDVLERNQVFEP.CLDAFPNLKDFISRFEGLE.ISAY.KSSRFLPRPVFT
Retrocopy FLGKQPWFLGDKIALVDFIAYDVLERNQVFEPKCLDAFPNLKDFISRFEGLE-ISAYTKSSRFLPRPVFT

Parental  KMAVWGNK
          KMAVWGNK
Retrocopy KMAVWGNK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	141.30 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	94.32 RPM
SRP007412_cerebellum	0.00 RPM	167.89 RPM
SRP007412_heart	0.00 RPM	234.78 RPM
SRP007412_kidney	0.00 RPM	137.20 RPM
SRP007412_liver	0.00 RPM	2033.54 RPM
SRP007412_testis	0.00 RPM	147.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1806 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1806 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1806 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3643
Pan troglodytes	retro_ptro_2468
Gorilla gorilla	retro_ggor_2459
Pongo abelii	retro_pabe_2990
Callithrix jacchus	retro_cjac_2463

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004970	1 retrocopy	retro_amel_1548,
Bos taurus	ENSBTAG00000016472	1 retrocopy	retro_btau_1181,
Equus caballus	ENSECAG00000024971	1 retrocopy	retro_ecab_1058,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Macaca mulatta	ENSMMUG00000019630	2 retrocopies	retro_mmul_1432, retro_mmul_1806 ,
Mustela putorius furo	ENSMPUG00000003658	1 retrocopy	retro_mputfur_758,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,
Pteropus vampyrus	ENSPVAG00000009559	1 retrocopy	retro_pvam_1047,
Tarsius syrichta	ENSTSYG00000007276	1 retrocopy	retro_tsyr_793,